Full-length cDNAs: more than just reaching the ends

Physiological Genomics - Tập 6 Số 2 - Trang 57-80 - 2001
Manjula Das1, Isabelle Harvey1, Lee Lee Chu1, Manisha Sinha1, Jerry Pelletier1,2
1Department of Biochemistry
2McGill Cancer Center McGill University Montreal, Quebec Canada H3G 1Y6

Tóm tắt

The development of functional genomic resources is essential to understand and utilize information generated from genome sequencing projects. Central to the development of this technology is the creation of high-quality cDNA resources and improved technologies for analyzing coding and noncoding mRNA sequences. The isolation and mapping of cDNAs is an entrée to characterizing the information that is of significant biological relevance in the genome of an organism. However, a bottleneck is often encountered when attempting to bring to full-length (or at least full-coding) a number of incomplete cDNAs in parallel, since this involves the nonsystematic, time consuming, and labor-intensive iterative screening of a number of cDNA libraries of variable quality and/or directed strategies to process individual clones (e.g., 5′ rapid amplification of cDNA ends). Here, we review the current state of the art in cDNA library generation, as well as present an analysis of the different steps involved in cDNA library generation.

Từ khóa


Tài liệu tham khảo

10.1038/343662a0

10.1007/BF01919535

10.1093/nar/21.20.4803

10.1093/nar/19.21.5901

10.1074/jbc.274.7.4377

10.1016/0014-5793(92)80988-S

10.1021/bi00154a010

Bassett JH, Rashbass P, Harding B, Forbes SA, Pannett AA, and Thakker RV.Studies of the murine homolog of the multiple endocrine neoplasia type 1 (MEN1) gene, men1.J Bone Miner Res14: 3–10, 1999.

10.1093/nar/17.8.2919

10.1016/0076-6879(87)52024-9

10.1016/0076-6879(87)52022-5

10.1016/0076-6879(89)80087-4

10.1074/jbc.270.6.2411

10.1002/j.1460-2075.1990.tb07399.x

10.1073/pnas.90.8.3496

10.1002/j.1460-2075.1994.tb06585.x

10.1101/gr.10.4.547

10.1038/250199a0

10.1111/j.1432-1033.1987.tb13439.x

10.1089/dna.1994.13.977

10.1006/abio.1994.1032

10.1002/j.1460-2075.1994.tb06668.x

10.1101/gr.6.9.791

10.1073/pnas.72.9.3580

10.1073/pnas.91.4.1256

10.1016/0092-8674(92)90519-I

10.1093/nar/18.14.4191

10.1016/0092-8674(92)90520-M

10.1074/jbc.271.15.8646

10.1006/jmbi.1997.0951

10.1126/science.282.5388.484

10.1006/geno.2000.6141

10.1006/geno.1996.0567

10.1073/pnas.95.2.520

10.1101/gr.145100

10.1016/0092-8674(89)90602-8

10.1021/bi00582a009

10.1093/nar/16.5.1999

10.1074/jbc.270.52.31225

10.1006/jmbi.1995.0635

10.1017/S1355838298971837

10.1093/nar/16.8.3141

Dib-Hajj F, Khan R, and Giedroc DP.Retroviral nucleocapsid proteins possess potent nucleic acid strand renaturation activity.Protein Sci2: 231–243, 1993.

10.1128/MCB.15.6.3363

10.1093/nar/19.19.5227

10.1016/0092-8674(76)90027-1

10.1101/gr.10.8.1230

10.1016/0092-8674(89)90053-6

10.1016/0003-2697(86)90286-1

Fresco LD and Buratowski S.Conditional mutants of the yeast mRNA capping enzyme show that the cap enhances, but is not required for, mRNA splicing.RNA2: 584–596, 1996.

10.1093/nar/19.24.6961

10.1016/0092-8674(77)90031-9

10.1007/BF02762340

10.1146/annurev.biochem.68.1.913

10.1016/S0014-5793(98)01411-2

10.1002/j.1460-2075.1994.tb06669.x

10.1016/S1097-2765(00)80065-9

10.1016/0378-1119(83)90230-5

10.1038/nbt0497-331

Hadzopoulou-Cladaras M, Felber BK, Cladaras C, Athanassopoulos A, Tse A, and Pavlakis GN.The rev (trs/art) protein of human immunodeficiency virus type 1 affects viral mRNA and protein expression via a cis-acting sequence in the env region.J Virol63: 1265–1274, 1989.

Hagenbuch B, Lubbert H, Stieger B, and Meier PJ.Expression of the hepatocyte Na+/bile acid cotransporter inXenopus laevisoocytes.J Biol Chem265: 5357–5360, 1990.

10.1016/0076-6879(83)00066-X

10.1016/0092-8674(88)90507-7

10.1093/nar/12.21.8235

10.1006/geno.2000.6187

10.1016/0006-291X(64)90255-4

10.1073/pnas.93.16.8175

10.1002/j.1460-2075.1994.tb06586.x

10.1073/pnas.73.9.3146

Hilton AA, Slavin AJ, Hilton DJ, and Bernard CC.Characterization of cDNA and genomic clones encoding human myelin oligodendrocyte glycoprotein.J Neurochem65: 309–318, 1995.

Hizi A, Leis JP, and Joklik WK.The RNA-dependent DNA polymerase of avian sarcoma virus B77. Binding of viral and nonviral ribonucleic acids to the α, β2, and αβ forms of the enzyme.J Biol Chem252: 6878–6884, 1977.

10.1016/0014-5793(76)80597-2

10.1073/pnas.160270997

10.1128/MCB.13.12.7476

10.1093/emboj/18.6.1642

10.1128/MCB.15.7.3864

Huber HE, McCoy JM, Seehra JS, and Richardson CC.Human immunodeficiency virus 1 reverse transcriptase. Template binding, processivity, strand displacement synthesis, and template switching.J Biol Chem264: 4669–4678, 1989.

10.1016/0022-2836(92)90975-P

10.1101/gad.3.9.1472

10.1006/viro.1994.1130

10.1021/bi00119a002

10.1039/b005999o

Khan R and Giedroc DP.Recombinant human immunodeficiency virus type 1 nucleocapsid (NCp7) protein unwinds tRNA.J Biol Chem267: 6689–6695, 1992.

Kienzle N, Young DB, Liaskou D, Buck M, Greco S, and Sculley TB.Intron retention may regulate expression of Epstein-Barr virus nuclear antigen 3 family genes.J Virol73: 1195–1204, 1999.

10.1093/nar/18.19.5705

10.1073/pnas.83.9.2850

10.1093/nar/15.20.8125

10.1128/MCB.7.10.3438

10.1007/s003359900171

Kullak-Ublick GA, Gerloff T, Hagenbuch B, Berr F, Meier PJ, and Stieger B.Expression of a rat liver phosphatidylcholine translocator inXenopus laevisoocytes.Hepatology23: 1254–1259, 1996.

10.1038/35057062

10.1093/nar/21.4.831

10.1093/nar/23.13.2434

Lawson TG, Cladaras MH, Ray BK, Lee KA, Abramson RD, Merrick WC, and Thach RE.Discriminatory interaction of purified eukaryotic initiation factors 4F plus 4A with the 5′ ends of reovirus messenger RNAs.J Biol Chem263: 7266–7276, 1988.

10.1128/MCB.10.7.3456

10.1002/j.1460-2075.1989.tb08401.x

10.1111/j.1365-2958.1992.tb02206.x

10.1101/gad.9.14.1766

10.1128/AAC.34.10.2009

Majumdar C, Abbotts J, Broder S, and Wilson SH.Studies on the mechanism of human immunodeficiency virus reverse transcriptase. Steady-state kinetics, processivity, and polynucleotide inhibition.J Biol Chem263: 15657–65, 1988.

10.1038/338254a0

Maniatis T, Kee SG, Efstratiadis A, and Kafatos FC.Amplification and characterization of a beta-globin gene synthesized in vitro.Cell8: 163–182, 1976.

10.1016/S0092-8674(00)80280-9

10.1016/0378-1119(94)90802-8

10.1101/gad.11.24.3306

10.1074/jbc.272.13.8628

10.1016/0092-8674(89)90404-2

Morrow JR.Hydrolytic cleavage of RNA catalyzed by metal ion complexes.Met Ions Biol Syst33: 561–592, 1996.

10.1101/gad.8.7.855

10.1006/jmbi.1994.1592

10.1073/pnas.92.6.2209

10.1073/pnas.89.7.2718

10.1128/AAC.31.10.1524

10.1128/MCB.19.2.1262

10.1128/MCB.2.2.161

Ouellette AJ and Ordahl CP.Extensive homology between poly(A)-containing mRNA and purified nominal poly(A)-lacking mRNA in mouse kidney.J Biol Chem256: 5104–5108, 1981.

10.1016/S0378-5955(98)00065-3

10.1093/emboj/16.24.7500

10.1073/pnas.88.5.1943

10.1021/bi00216a029

10.1038/334320a0

10.1074/jbc.274.3.1635

10.1016/S0378-1119(98)00154-1

10.1073/pnas.86.6.1836

Robbins PF, El-Gamil M, Li YF, Fitzgerald EB, Kawakami Y, and Rosenberg SA.The intronic region of an incompletely spliced gp100 gene transcript encodes an epitope recognized by melanoma-reactive tumor-infiltrating lymphocytes.J Immunol159: 303–308, 1997.

10.1128/MCB.9.2.469

10.1038/76118

10.1093/nar/2.12.2365

10.1073/pnas.73.10.3418

10.1016/0012-1606(77)90109-9

10.1002/j.1460-2075.1991.tb07994.x

10.1093/nar/27.21.e31

10.1093/nar/28.10.e47

10.1016/0092-8674(87)90212-1

10.1016/S0959-437X(96)80083-9

10.1038/35057141

10.1007/BF00986963

10.1139/w98-020

10.1073/pnas.91.20.9228

10.1016/S0079-6603(08)60614-5

10.1128/MCB.18.12.7371

10.1021/bi00872a033

10.1016/0003-2697(87)90241-7

10.1016/S0378-1119(00)00557-6

10.1006/geno.2000.6076

10.1073/pnas.84.14.4767

10.7164/antibiotics.42.107

10.1089/aid.1994.10.983

10.1073/pnas.85.6.1777

10.1006/viro.1996.8407

10.1016/0005-2787(65)90044-4

10.1073/pnas.89.20.9823

Tsuchihashi Z and Brown PO.DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein.J Virol68: 5863–5870, 1994.

10.1073/pnas.85.5.1364

10.1006/bbrc.1997.6892

10.1016/0092-8674(79)90244-7

10.1073/pnas.91.9.3554

10.1126/science.1058040

Verma IM.Studies on reverse transcriptase of RNA tumor viruses. I. Localization of thermolabile DNA polymerase and RNase H activities on one polypeptide.J Virol15: 121–126, 1975.

10.1073/pnas.97.8.4162

10.1006/abio.1997.2530

Wu W, Henderson LE, Copeland TD, Gorelick RJ, Bosche WJ, Rein A, and Levin JG.Human immunodeficiency virus type 1 nucleocapsid protein reduces reverse transcriptase pausing at a secondary structure near the murine leukemia virus polypurine tract.J Virol70: 7132–7142, 1996.

You JC and McHenry CS.Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription.J Biol Chem269: 31491–31495, 1994.

10.1083/jcb.128.3.415

10.1101/gr.140200

Zhumabayeva B, Chang C, McKinley J, Diatchenko L, and Siebert PD.Generation of full-length cDNA libraries enriched for differentially expressed genes for functional genomics.Biotechniques30: 512–516, 518–520, 2001.